Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1821

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 11795
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36


Found at i:5185 original size:19 final size:19

Alignment explanation


    Indices: 5161--5197  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       5151 AATAAGTCTT

                               
       5161 AAGTATATATAGTTTTATC
          1 AAGTATATATAGTTTTATC

                              
       5180 AAGTATATATAGTTTTAT
          1 AAGTATATATAGTTTTAT

       5198 TATTATTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49


Consensus pattern (19 bp):   
AAGTATATATAGTTTTATC

Found at i:5878 original size:17 final size:18

Alignment explanation


    Indices: 5856--5889  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       5846 ATTTTTCTTT

                              
       5856 TATAGTTACA-TTTTTTA
          1 TATAGTTACACTTTTTTA

                   *         
       5873 TATAGTTTCACTTTTTT
          1 TATAGTTACACTTTTTT

       5890 TTTTTGTAGC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62


Consensus pattern (18 bp):   
TATAGTTACACTTTTTTA

Found at i:5993 original size:30 final size:29

Alignment explanation


    Indices: 5932--5993  Score: 72
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       5922 TACATTCAAA

                        *            *   
       5932 TTTTTCATTGAACAAAAATTCTTGTGCTT
          1 TTTTTCATTGAAAAAAAATTCTTGTACTT

                      *          *        
       5961 TTTTTCATCTTAAAAAAAATTTTTGTA-TT
          1 TTTTTCAT-TGAAAAAAAATTCTTGTACTT

                
       5990 TTTT
          1 TTTT

       5994 AGTAACTTAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  29   14  0.50
  30   14  0.50

ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55


Consensus pattern (29 bp):   
TTTTTCATTGAAAAAAAATTCTTGTACTT
Done.